{"action":"created","issue":{"url":"https://api.github.com/repos/soedinglab/hh-suite/issues/54","repository_url":"https://api.github.com/repos/soedinglab/hh-suite","labels_url":"https://api.github.com/repos/soedinglab/hh-suite/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/soedinglab/hh-suite/issues/54/comments","events_url":"https://api.github.com/repos/soedinglab/hh-suite/issues/54/events","html_url":"https://github.com/soedinglab/hh-suite/issues/54","id":223810727,"number":54,"title":"Zero SS scores when using both pdb and pfam","user":{"login":"jamespjh","id":55009,"avatar_url":"https://avatars3.githubusercontent.com/u/55009?v=3","gravatar_id":"","url":"https://api.github.com/users/jamespjh","html_url":"https://github.com/jamespjh","followers_url":"https://api.github.com/users/jamespjh/followers","following_url":"https://api.github.com/users/jamespjh/following{/other_user}","gists_url":"https://api.github.com/users/jamespjh/gists{/gist_id}","starred_url":"https://api.github.com/users/jamespjh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamespjh/subscriptions","organizations_url":"https://api.github.com/users/jamespjh/orgs","repos_url":"https://api.github.com/users/jamespjh/repos","events_url":"https://api.github.com/users/jamespjh/events{/privacy}","received_events_url":"https://api.github.com/users/jamespjh/received_events","type":"User","site_admin":false},"labels":[{"id":207354449,"url":"https://api.github.com/repos/soedinglab/hh-suite/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":{"login":"martin-steinegger","id":1413571,"avatar_url":"https://avatars1.githubusercontent.com/u/1413571?v=3","gravatar_id":"","url":"https://api.github.com/users/martin-steinegger","html_url":"https://github.com/martin-steinegger","followers_url":"https://api.github.com/users/martin-steinegger/followers","following_url":"https://api.github.com/users/martin-steinegger/following{/other_user}","gists_url":"https://api.github.com/users/martin-steinegger/gists{/gist_id}","starred_url":"https://api.github.com/users/martin-steinegger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martin-steinegger/subscriptions","organizations_url":"https://api.github.com/users/martin-steinegger/orgs","repos_url":"https://api.github.com/users/martin-steinegger/repos","events_url":"https://api.github.com/users/martin-steinegger/events{/privacy}","received_events_url":"https://api.github.com/users/martin-steinegger/received_events","type":"User","site_admin":false},"assignees":[{"login":"martin-steinegger","id":1413571,"avatar_url":"https://avatars1.githubusercontent.com/u/1413571?v=3","gravatar_id":"","url":"https://api.github.com/users/martin-steinegger","html_url":"https://github.com/martin-steinegger","followers_url":"https://api.github.com/users/martin-steinegger/followers","following_url":"https://api.github.com/users/martin-steinegger/following{/other_user}","gists_url":"https://api.github.com/users/martin-steinegger/gists{/gist_id}","starred_url":"https://api.github.com/users/martin-steinegger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martin-steinegger/subscriptions","organizations_url":"https://api.github.com/users/martin-steinegger/orgs","repos_url":"https://api.github.com/users/martin-steinegger/repos","events_url":"https://api.github.com/users/martin-steinegger/events{/privacy}","received_events_url":"https://api.github.com/users/martin-steinegger/received_events","type":"User","site_admin":false}],"milestone":null,"comments":22,"created_at":"2017-04-24T12:56:11Z","updated_at":"2017-06-16T09:21:06Z","closed_at":null,"body":"```\r\nhh-suite commit ID  b1aa73afae4811c7\r\nOperating system: linux, compiler: gnu 4.9.2\r\n```\r\n\r\nHi,\r\n\r\nWhen using both pdb and pfam:\r\n\r\n`hhsearch  -d /home/ucgajhe/levine/databases/pdb70/pdb70 -ssm 4 -cpu 12 -o /home/ucgajhe/Scratch/Levine/results/test_YPR199C/YPR199C.0.ssw11.hhr -i /home/ucgajhe/Scratch/Levine/results/test_YPR199C/YPR199C.0.ss.a3m -v 2 -p 0 -cov 50 -ssw 0.11 -Z 5000 -d /home/ucgajhe/levine/databases/pfamA_30/pfam`\r\n\r\nwe observe zero secondary structure scores for both PDB matches and PFAM matches:\r\n\r\n```\r\nNo Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM\r\n  1 1gd2_E Transcription factor PA  98.7 3.4E-10 6.3E-15   83.8   8.4   68   11-81      1-68  (70)\r\n  2 1sse_B AP-1 like transcription  98.7 2.3E-11 4.2E-16   97.0   0.0   60  235-294    26-85  (86)\r\n  3 1gu4_A CAAT/enhancer binding p  98.1 2.5E-07 4.5E-12   69.3   9.7   61   14-77     11-71  (78)\r\n  4 PF08601.7 ; PAP1 ; Transcripti  97.9   3E-08 5.5E-13   97.1   0.0   56  236-291   298-355 (356)\r\n  5 1hjb_A Ccaat/enhancer binding   97.7   1E-07 1.9E-12   73.4   0.0   61   15-78     12-72  (87)\r\n  6 1ci6_A Transcription factor AT  97.5 2.9E-07 5.3E-12   65.6   0.0   57   18-77      2-58  (63)\r\n  7 PF00170.18 ; bZIP_1 ; bZIP tra  97.5 3.5E-07 6.5E-12   64.3   0.0   58   18-78      5-62  (64)\r\n  8 2dgc_A Protein (GCN4); basic d  97.5 4.4E-07   8E-12   64.4   0.0   57   15-74      6-62  (63)\r\n  9 2wt7_A Proto-oncogene protein   97.4 6.9E-07 1.3E-11   63.0   0.0   57   18-77      2-58  (63)\r\n 10 1jnm_A Proto-oncogene C-JUN; B  97.3 1.2E-06 2.2E-11   61.0   0.0   57   19-78      2-58  (62)\r\n 11 1dh3_A Transcription factor CR  97.2 1.7E-06 3.1E-11   59.9   0.0   52   19-73      2-53  (55)\r\n 12 PF07716.12 ; bZIP_2 ; Basic re  97.1 2.7E-06 4.9E-11   58.3   0.0   51   17-70      4-54  (55)\r\n 13 1t2k_D Cyclic-AMP-dependent tr  97.1 2.8E-06 5.2E-11   59.0   0.0   55   19-76      2-56  (61)\r\n 14 3a5t_A Transcription factor MA  97.1   4E-06 7.2E-11   68.2   0.0   62   18-82     37-98  (107)\r\n 15 2wt7_B Transcription factor MA  97.0 6.5E-06 1.2E-10   64.3   0.0   60   18-80     27-86  (90)\r\n 16 PF03131.14 ; bZIP_Maf ; bZIP M  96.9 9.6E-06 1.8E-10   62.1   0.0   58   18-78     30-87  (90)\r\n 17 5apu_A General control protein  96.5 0.00019 3.5E-09   59.1   3.2   48   19-73     46-93  (95)\r\n 18 2oxj_A Hybrid alpha/beta pepti  94.6   0.029 5.3E-07   38.0   4.4   32   39-73      1-32  (34)\r\n 19 2r2v_A GCN4 leucine zipper; co  94.4   0.036 6.6E-07   38.0   4.2   32   39-73      1-32  (34)\r\n 20 PF16689.2 ; APC_N_CC ; Coiled-  94.2  0.0059 1.1E-07   44.5   0.0   43   39-84      1-43  (52)\r\n 21 4c46_A General control protein  94.0  0.0079 1.4E-07   47.9   0.0   51   18-72     26-76  (76)\r\n 22 1kd8_B GABH BLL, GCN4 acid bas  93.7   0.011   2E-07   41.0   0.0   35   39-76      1-35  (36)\r\n 23 3w92_A Thioester coiled coil p  93.3   0.015 2.8E-07   39.4   0.0   31   40-73      1-31  (32)\r\n 24 1deb_A APC protein, adenomatou  93.3   0.015 2.8E-07   43.2   0.0   43   38-83      2-44  (54)\r\n 25 2wq1_A General control protein  92.6   0.025 4.5E-07   38.6   0.0   31   40-73      1-31  (33)\r\n 26 3c3g_A Alpha/beta peptide with  92.3    0.03 5.4E-07   38.2   0.0   31   40-73      1-31  (33)\r\n```\r\n\r\nbut when running with PDB only, we get nonzero scores for all matches.\r\n\r\nI note that the PDB database download includes SS data, but PFAM does not:\r\n\r\n```\r\n\r\nNo 10\r\n>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D\r\nProbab=97.47  E-value=4.4e-07  Score=64.37  Aligned_cols=57  Identities=26%  Similarity=0.323  Sum_probs=45.1  Template_Neff=9.500\r\n\r\nQ ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\r\nQ YPR199C          15 LTPPKNKRAAQLRASQNAFRKRKLERLEELEKKEAQLTVTNDQIHILKKENELLHFMLRS   74 (294)\r\nQ Consensus        15 ~~~~k~KRKaQNRaAQkAFRERKE~rlkeLE~kl~ele~~~~~~~~L~~EnE~Lr~~n~e   74 (294)\r\n                      ....+.+|+.+||.||+.+|+||..++.+||.++..|+..+   ..|..+++.|+..+..\r\nT Consensus         6 ~~~~~~~kr~rnr~~~~~~R~rk~~~~~~le~~v~~l~~~~---~~l~~~~~~l~~~~~~   62 (63)\r\nT 2dgc_A            6 SSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKN---YHLENEVARLKKLVGE   62 (63)\r\nT ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHC---\r\nT ss_pred             cccHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHh\r\nConfidence            34566778899999999999999999999999999999888   7888888888876654\r\n\r\n\r\nNo 11\r\n>PF00170.19 ; bZIP_1 ; bZIP transcription factor\r\nProbab=97.45  E-value=4.9e-07  Score=63.79  Aligned_cols=58  Identities=28%  Similarity=0.290  Sum_probs=51.1  Template_Neff=9.800\r\n\r\nQ ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\r\nQ YPR199C          18 PKNKRAAQLRASQNAFRKRKLERLEELEKKEAQLTVTNDQIHILKKENELLHFMLRSLLTE   78 (294)\r\nQ Consensus        18 ~k~KRKaQNRaAQkAFRERKE~rlkeLE~kl~ele~~~~~~~~L~~EnE~Lr~~n~el~~e   78 (294)\r\n                      ++.+|+.+||.||+.||+||..++.+||.++..|+...   ..|..+++.|+..+..|..+\r\nT Consensus         5 k~~rr~~~nr~~~~~~R~rk~~~~~~Le~~~~~L~~~~---~~l~~~~~~l~~e~~~L~~~   62 (64)\r\nT GBF1_ARATH/220    5 KRQKRKQSNRESARRSRLRKQAECEQLQQRVESLSNEN---QSLRDELQRLSSECDKLKSE   62 (64)\r\nConfidence            56788999999999999999999999999999999888   77888888888887776554\r\n```\r\n\r\nWe note that secondary structure nonzero matches are found in the web-search tool, but that the downloadable version of hh-pfam does not have any SS info in it.\r\n\r\nMost confusing of all, though, is why PDB matches become zero SS score when PFAM is present.\r\n\r\nI think this might have something to do with the code in https://github.com/soedinglab/hh-suite/blob/master/src/hhviterbirunner.cpp\r\n\r\n``` cpp\r\n   int ss_hmm_mode = HMM::computeScoreSSMode(q_simd->GetHMM(0), t_hmm_simd->GetHMM(0));\r\n    for(size_t i = 1; i < maxres; i++){\r\n        ss_hmm_mode = std::min(ss_hmm_mode,\r\n                               HMM::computeScoreSSMode(q_simd->GetHMM(0), t_hmm_simd->GetHMM(i)));\r\n    }\r\n```\r\n\r\nand this:\r\n\r\nhttps://github.com/soedinglab/hh-suite/blob/master/src/hhhmm.cpp\r\n\r\n``` cpp\r\nint HMM::computeScoreSSMode( HMM *q,  HMM *t){\r\n\tint returnMode = HMM::NO_SS_INFORMATION;\r\n\tif      (q->nss_pred>=0 && t->nss_dssp>=0) returnMode=HMM::PRED_DSSP;\r\n\telse if (q->nss_dssp>=0 && t->nss_pred>=0) returnMode=HMM::DSSP_PRED;\r\n\telse if (q->nss_pred>=0 && t->nss_pred>=0) returnMode=HMM::PRED_PRED;\r\n\treturn returnMode;\r\n}\r\n```\r\n\r\nwhich takes a minimum across the available data, so would result in zero SS for PDB when PFAM is present.\r\n\r\nAny thoughts?"},"comment":{"url":"https://api.github.com/repos/soedinglab/hh-suite/issues/comments/308977532","html_url":"https://github.com/soedinglab/hh-suite/issues/54#issuecomment-308977532","issue_url":"https://api.github.com/repos/soedinglab/hh-suite/issues/54","id":308977532,"user":{"login":"martin-steinegger","id":1413571,"avatar_url":"https://avatars1.githubusercontent.com/u/1413571?v=3","gravatar_id":"","url":"https://api.github.com/users/martin-steinegger","html_url":"https://github.com/martin-steinegger","followers_url":"https://api.github.com/users/martin-steinegger/followers","following_url":"https://api.github.com/users/martin-steinegger/following{/other_user}","gists_url":"https://api.github.com/users/martin-steinegger/gists{/gist_id}","starred_url":"https://api.github.com/users/martin-steinegger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martin-steinegger/subscriptions","organizations_url":"https://api.github.com/users/martin-steinegger/orgs","repos_url":"https://api.github.com/users/martin-steinegger/repos","events_url":"https://api.github.com/users/martin-steinegger/events{/privacy}","received_events_url":"https://api.github.com/users/martin-steinegger/received_events","type":"User","site_admin":false},"created_at":"2017-06-16T09:21:06Z","updated_at":"2017-06-16T09:21:06Z","body":"SS scores can be negative. You could check the SS structure alignment of this negative scoring hits.\r\n\r\nThe 0 at the SS scoring can still occur when mixing SS types at the target db. (e.g. If some hmms don't have a SS structure or if some have just DSSP and other just Predictions)\r\n\r\nI'm currently busy with writing my thesis. I might change the 0 score problem afterwards. "}}
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